The accuracy of genotypes for large deletions was assessed against previous array based analyses20 (Supplementary Fig. 11). The genotype error rate across all allele frequencies and genotypes was < 1%, with the accuracy of heterozygous genotypes at low (MAF < 3%), intermediate (MAF ~50%) and high frequency (MAF > 97%) variants estimated at 86%, 97% and 83% respectively. The greater apparent genotype accuracy of structural variants compared to SNPs in the low coverage project reflects the increased number of informative reads per individual for variants of large size and a bias in the known large deletion genotype set for larger, easier to genotype variants.
